DSC 520 Final Project
Courtney Klatt
11/19/2020
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## Source : https://maps.googleapis.com/maps/api/geocode/json?address=Florida&key=xxxIntroduction
Deep sea coral reefs are fairly unknown to the general public. When most people think of coral reefs, they imagine the shallow, tropical coral reefs. Deep sea coral reefs, also known as cold-water coral reefs, are found at depths between 200 and 1500 meters (Rogers 2004) and temperatures from 4 to 12 degrees Celsius (Roberts 2006). These reefs are home to approximately two thirds of the coral species in the world, yet they are largely understudied due to their inaccessibility (Roberts 2004). Cold-water corals, similarly to their tropical counterparts, grow very slowly. Many species will grow only a few millimeters each year.
Deep sea coral reefs have large commercial importance due to the variety of commonly consumed organisms that live there. These reefs are breeding grounds for many species of fish and crustaceans, including cod, mackerel, crab, grouper, and even sharks (Krieger 2002). Additionally, many important compounds that are used to reduce inflammation and fight cancerous tumors can be found in species from these reefs (Team 2018).
Human activity, however, greatly threatens these reefs. Fishing, especially trawling, can damage or even completely destroy these ecosystems by dragging along the substrate (Team 2018). Figure 1 shows a reef before and after trawling. Additional threats to coral reefs include oil and gas exploration in the deep sea, especially when spills occur releasing pollutants that can kill reef organisms, and ocean acidification, which makes it more difficult for coral skeletons to grow and can weaken existing skeletons (Team 2018).
Deep sea coral reef before and after trawling. The top photo shows a rugose reef with vast biodiversity including fish, corals, and other invertebrates. The bottom photo shows a decimated reef that was flattened by trawling. (Team 2018)
Problem Statement
In this project I will compare the health of, threats to, and future outlook of deep sea coral reefs around the United States.
Data and Methodology
For this project, I first used deep sea coral reef data (NOAA 2017). Next, I removed the data points that were collected prior to 2000, as is it quite possible that those data points no longer accurately represent the current biodiversity. Next, I removed the columns that were not pertinent to my study, and created databases based on location. I then narrowed these databases down to 15, all of which had at least 1000 individual data points. From there, I was able to use ggmap to plot the mean latitudes and longitudes for each database to show the approximate locations that the data came from. Next, I used plot_ly to create bar charts of the biodiversity at each study site. After that, I used the count() function with each database to get the total number of data points at each location, and the unique() function to get the number of distinct species at each location. This data was displayed in a table. A correlation test was performed to analyze the correlation between number of unique species and total number of observations. Then, I used the fishing and aquaculture data (Tzer 2018)(Aché 2020). This data was plotted for each database using ggplot to show the change in American exports of crustaceans and fish from 2000-2015. A Pearson correlation test was used to compare the relationship between fishing and aquaculture in countries around the world.
Maps
The following maps plot the approximate center of the data sets for each location used in this study. The zoom out function must be used to fully view the scope of each map in the html format.
Hawaii_MapAlaska_MapOlympic_Coast_MapSt_George_MapPioneer_MapCordell_MapDavidson_MapMonterey_MapRodriguez_MapChannel_Islands_MapHidden_MapEureka_MapGulf_of_Mexico_MapViosca_MapPourtales_MapCape_Canaveral_MapBiodiversity
Below are charts that represent the species diversity at each location in the study.
Hawaii_Biodiversity## Warning: `arrange_()` is deprecated as of dplyr 0.7.0.
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## Call `lifecycle::last_warnings()` to see where this warning was generated.Alaska_BiodiversityOlmypic_Coast_BiodiversitySt_George_BiodiversityPioneer_BiodiversityCordell_BiodiversityDavidson_BiodiversityMonterey_BiodiversityRodriguez_BiodiversityChannel_Islands_BiodiversityHidden_BiodiversityEureka_BiodiversityGulf_of_Mexico_BiodiversityViosca_BiodiversityPourtales_BiodiversityCape_Canaveral_BiodiversityBelow is the comparison of number of species observed at each site to the total count of individuals at each location.
| Location | Number of Species | Total Observations |
|---|---|---|
| Hawaii | 14 | 42503 |
| Alaska | 13 | 39399 |
| Olympic_Coast | 5 | 14079 |
| St_George | 7 | 7005 |
| Pioneer | 13 | 28135 |
| Cordell | 10 | 5016 |
| Davidson | 10 | 40128 |
| Monterey | 8 | 1903 |
| Rodriguez | 9 | 18713 |
| Channel_Islands | 7 | 15768 |
| Hidden | 11 | 3294 |
| Eureka | 7 | 3898 |
| Gulf_of_Mexico | 12 | 1465 |
| Viosca | 4 | 9986 |
| Pourtales | 10 | 5798 |
| Cape_Canaveral | 10 | 2707 |
Below is a correlation analysis of the biodiversity at each site comparing the number of species observed to the total number of observations at each site.
biodiversity_correlation## [,1] [,2]
## [1,] 1.0000000 0.4656524
## [2,] 0.4656524 1.0000000This correlation test compares the number of species found at each location by the number of observations per location to see if greater observations leads to greater biodiversity. There is not a strong correlation.
Fishing and Aquaculture
American_Fishing_Exports_Fish_Plot## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
The fishing exports data shows a large increase in fish exports from the United States from 2000 to 2015.
American_Fishing_Exports_Crustacean_Plot## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
The crustacean exports data shows a large increase in crustacean exports from the United States from 2000 to 2015.
Aquaculture_Capture_Correlation##
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## data: aqua$Capture and aqua$Aquaculture
## t = 35.511, df = 215, p-value < 2.2e-16
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
## 0.9021810 0.9415777
## sample estimates:
## cor
## 0.9243043This Pearson’s test suggests that there is a strong positive correlation between fishing and aquaculture, meaning that countries with high fishing rates also have a high rate of aquaculture. This means that an increase in aquaculture efforts by a country does not mean that that effort is replacing fishing effort, but rather adding to the fishing efforts. The United States had a capture value of 4,931,017 and an aquaculture value of 444,369.
Implications
Biodiversity
The graphs of different species observed at each site are all quite different. This suggests that there is a great range of biodiversity at each site, meaning that the different locations are all diverse in their own way.
The lack of strong correlation between number of observations and species count suggests that our data points accurately represent the populations and there is not a significant difference between biodiversity at the different data collection locations.
Each site had a least 4 species observed. Due to the limited descriptions of deep sea reef species and limited survey data, it is likely that more species are present. The prevalence of multiple species at each site and mutliple different types of species (hard corals, soft corals, sponges, etc.) suggests that these reefs are successfully maintaining biodiversity, which is promising for the future of these reefs.
Fishing and Aquaculture
The crustacean and fish export plots show large increases in exports of both seafood types over the 15-year time span. This means that fishing efforts on deep-sea reefs have greatly increased over this time, which removes biodiversity and causes damage to deep sea coral reefs.
A common thought among biologists is that we can increase sustainability by replacing some fishing efforts with aquaculture. However, the aquaculture vs. capture data suggests that this is not the case, and countries with high rates of aquaculture also have high rates of fishing. However, this still is better for the reefs than if all consumption came from capture alone.
This fishing and aquaculture data suggests that these reefs will continue to be threatened by destructive fishing practices, such as trawling. In order to protect these reefs, we must invest in more sustainable fishing practices and/or better aquaculture practices.
Limitations and Future Steps
One limitation of this study comes from lack of data. Deep sea coral reefs are very difficult to access due to their location and the financial requirements to access these depths. They are also extremely understudied and many of species present on these reefs have not been described. While the data set I used had over 50,000 initial data points, a large proportion of those come from prior to the year 2000, and therefore may not accurately reflect the current state of these reefs. Due to the unreliability of these data points, they had to be removed. Additionally, I removed data points from locations that had fewer than 1000 data points, as these data sets would not accurately represent the biodiversity at those sites. This limited my analyses to just U.S. locations.
In future studies I would suggest locating data sets that have a broader range of countries represented. This would allow for a more global comparison of deep sea reef biodiversity, threats, and future outlook.
Conclusion
This study shared that there is high biodiversity and overall population at each location that was analyzed. The United States does have laws in place to regulate fishing and reduce overfishing (Fisheries 2019). Furthermore, NOAA provides information for fishermen about best practices to reduce bycatch and destruction of habitat (Fisheries). Despite the current health of these reefs and the protocols in place to protect the biodiversity and physical structure of the reefs, the rising demand for, and therefore threat of, fishing will have a toll on these reefs. In addition, the increase in ocean acidification puts these reefs at greater danger, as they will have more difficulty growing and keeping their carbon skeletons intact (Ocean acidification).
Our country, and all countries around the world, need to work to reduce our carbon emissions to decrease the threat to these vital reef ecosystems. Furthermore, we must find less destructive and more sustainable fishing practices, and increase the efficacy of our aquaculture systems.
References:
Aché, M. (2020, July 17). Fishing_industry_by_country. Retrieved November 11, 2020, from https://www.kaggle.com/mathurinache/fishing-industry-by-country
Fisheries, N. (2019, September 13). Fishing Gear: Bottom Trawls. Retrieved November 18, 2020, from https://www.fisheries.noaa.gov/national/bycatch/fishing-gear-bottom-trawls
Fisheries, N. (n.d.). Laws & Policies. Retrieved November 20, 2020, from https://www.fisheries.noaa.gov/topic/laws-policies
Krieger KJ and Wing B. 2002. Megafauna associations with deepwater corals (Primnoa spp.) in the Gulf of Alaska. Hydrobiologia 471: 83–90
Noaa. (2017, August 28). Deep Sea Corals. Retrieved November 12, 2020, from https://www.kaggle.com/noaa/deep-sea-corals?select=deep_sea_corals.csv
Ocean acidification. (n.d.). Retrieved November 20, 2020, from https://www.noaa.gov/education/resource-collections/ocean-coasts/ocean-acidification
Roberts, J., Wheeler, A. J., & Freiwald, A. (2006). Reefs of the Deep: The Biology and Geology of Cold-Water Coral Ecosystems. Science, 312.
Roberts, S., & Hirshfield, M. (2004). Deep-sea corals: Out of sight, but no longer out of mind. Frontiers in Ecology and the Environment, 2(3), 123-130.
Rogers, A., PhD. (2004). The Biology, Ecology and Vulnerability of Deep-Water Coral Reefs. Retrieved from https://portals.iucn.org/library/efiles/documents/Rep-2004-002.pdf
Team, T. (2018, December 18). Deep-sea Corals. Retrieved November 15, 2020, from https://ocean.si.edu/ecosystems/coral-reefs/deep-sea-corals
Tzer, Z. (2018, July 02). Global Aquaculture Imports and Exports. Retrieved November 11, 2020, from https://www.kaggle.com/zhengtzer/global-fisheries-aquaculture-department